LAMMPS (4 Nov 2022)
# two monomer nylon example
# reaction produces a condensed water molecule

units real

boundary p p p

atom_style full

kspace_style pppm 1.0e-4

pair_style lj/class2/coul/long 8.5

angle_style class2

bond_style class2

dihedral_style class2

improper_style class2

read_data tiny_nylon.data   extra/bond/per/atom 5    extra/angle/per/atom 15   extra/dihedral/per/atom 15   extra/improper/per/atom 25   extra/special/per/atom 25
Reading data file ...
  orthogonal box = (-25 -25 -25) to (25 25 25)
  1 by 2 by 2 MPI processor grid
  reading atom labelmap ...
  reading bond labelmap ...
  reading angle labelmap ...
  reading dihedral labelmap ...
  reading improper labelmap ...
  reading atoms ...
  44 atoms
  reading velocities ...
  44 velocities
  scanning bonds ...
  9 = max bonds/atom
  scanning angles ...
  21 = max angles/atom
  scanning dihedrals ...
  29 = max dihedrals/atom
  scanning impropers ...
  29 = max impropers/atom
  reading bonds ...
  42 bonds
  reading angles ...
  74 angles
  reading dihedrals ...
  100 dihedrals
  reading impropers ...
  44 impropers
Finding 1-2 1-3 1-4 neighbors ...
  special bond factors lj:    0        0        0       
  special bond factors coul:  0        0        0       
     4 = max # of 1-2 neighbors
     6 = max # of 1-3 neighbors
    12 = max # of 1-4 neighbors
    41 = max # of special neighbors
  special bonds CPU = 0.000 seconds
  read_data CPU = 0.008 seconds

velocity all create 300.0 4928459 dist gaussian

molecule mol1 rxn1_stp1_unreacted.molecule_template
Read molecule template mol1:
  1 molecules
  0 fragments
  18 atoms with max type 8
  16 bonds with max type 10
  25 angles with max type 28
  23 dihedrals with max type 36
  2 impropers with max type 3
molecule mol2 rxn1_stp1_reacted.molecule_template
Read molecule template mol2:
  1 molecules
  0 fragments
  18 atoms with max type 9
  17 bonds with max type 13
  31 angles with max type 27
  39 dihedrals with max type 33
  0 impropers with max type 0
molecule mol3 rxn1_stp2_unreacted.molecule_template
Read molecule template mol3:
  1 molecules
  0 fragments
  15 atoms with max type 9
  14 bonds with max type 13
  25 angles with max type 27
  30 dihedrals with max type 33
  0 impropers with max type 0
molecule mol4 rxn1_stp2_reacted.molecule_template
Read molecule template mol4:
  1 molecules
  0 fragments
  15 atoms with max type 11
  13 bonds with max type 15
  19 angles with max type 29
  16 dihedrals with max type 32
  2 impropers with max type 13

thermo 50

# dump 1 all xyz 1 test_vis.xyz

fix myrxns all bond/react stabilization yes statted_grp .03   react rxn1 all 1 0.0 2.9 mol1 mol2 rxn1_stp1_map   react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map
WARNING: Fix bond/react: Atom affected by reaction rxn2 is too close to template edge (../fix_bond_react.cpp:2624)
dynamic group bond_react_MASTER_group defined
dynamic group statted_grp_REACT defined

fix 1 statted_grp_REACT nvt temp 300 300 100

# optionally, you can customize behavior of reacting atoms,
# by using the internally-created 'bond_react_MASTER_group', like so:
fix 4 bond_react_MASTER_group temp/rescale 1 300 300 10 1

thermo_style custom step temp press density f_myrxns[1] f_myrxns[2]

# restart 100 restart1 restart2

run 10000

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

Your simulation uses code contributions which should be cited:

- fix bond/react: reacter.org doi:10.1016/j.polymer.2017.09.038, doi:10.1021/acs.macromol.0c02012

@Article{Gissinger17,
 author = {J. R. Gissinger and B. D. Jensen and K. E. Wise},
 title = {Modeling Chemical Reactions in Classical Molecular Dynamics Simulations},
 journal = {Polymer},
 year =    2017,
 volume =  128,
 pages =   {211--217}
}

@Article{Gissinger20,
 author = {J. R. Gissinger, B. D. Jensen, K. E. Wise},
 title = {{REACTER}: A Heuristic Method for Reactive Molecular Dynamics},
 journal = {Macromolecules},
 year =    2020,
 volume =  53,
 number =  22,
 pages =   {9953--9961}
}

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

PPPM initialization ...
  using 12-bit tables for long-range coulomb (../kspace.cpp:342)
  G vector (1/distance) = 0.05345967
  grid = 2 2 2
  stencil order = 5
  estimated absolute RMS force accuracy = 0.040225597
  estimated relative force accuracy = 0.00012113819
  using double precision KISS FFT
  3d grid and FFT values/proc = 252 2
Generated 55 of 55 mixed pair_coeff terms from sixthpower/geometric mixing rule
Neighbor list info ...
  update: every = 1 steps, delay = 0 steps, check = yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 10.5
  ghost atom cutoff = 10.5
  binsize = 5.25, bins = 10 10 10
  2 neighbor lists, perpetual/occasional/extra = 1 1 0
  (1) pair lj/class2/coul/long, perpetual
      attributes: half, newton on
      pair build: half/bin/newton
      stencil: half/bin/3d
      bin: standard
  (2) fix bond/react, occasional, copy from (1)
      attributes: half, newton on
      pair build: copy
      stencil: none
      bin: none
WARNING: Inconsistent image flags (../domain.cpp:819)
Per MPI rank memory allocation (min/avg/max) = 33.66 | 33.88 | 34.43 Mbytes
   Step          Temp          Press         Density      f_myrxns[1]    f_myrxns[2]  
         0   300            346.78165      0.0034851739   0              0            
        50   283.51963     -47.16359       0.0034851739   1              0            
       100   256.04648      21.778898      0.0034851739   1              1            
       150   450.78138     -11.7887        0.0034851739   1              1            
       200   400.15754      49.489858      0.0034851739   1              1            
       250   347.06066      68.952063      0.0034851739   1              1            
       300   291.89228     -1.5986302      0.0034851739   1              1            
       350   290.25995      17.634558      0.0034851739   1              1            
       400   234.89168      26.36452       0.0034851739   1              1            
       450   305.80709     -28.923896      0.0034851739   1              1            
       500   375.19218     -37.024375      0.0034851739   1              1            
       550   321.86944     -4.6961825      0.0034851739   1              1            
       600   307.2639      -31.393161      0.0034851739   1              1            
       650   255.95833      8.4995589      0.0034851739   1              1            
       700   294.54665     -17.06105       0.0034851739   1              1            
       750   273.08231     -10.7175        0.0034851739   1              1            
       800   249.69175      9.9777684      0.0034851739   1              1            
       850   307.71806     -6.9950047      0.0034851739   1              1            
       900   367.39855      9.9874984      0.0034851739   1              1            
       950   327.57334     -4.702978       0.0034851739   1              1            
      1000   348.85247      15.763492      0.0034851739   1              1            
      1050   328.94435     -35.031279      0.0034851739   1              1            
      1100   283.23971     -16.937443      0.0034851739   1              1            
      1150   266.69676      42.308482      0.0034851739   1              1            
      1200   244.61493     -8.2911432      0.0034851739   1              1            
      1250   206.68495      6.6280166      0.0034851739   1              1            
      1300   257.83339     -7.0826264      0.0034851739   1              1            
      1350   358.0875      -7.602474       0.0034851739   1              1            
      1400   353.66614      18.091914      0.0034851739   1              1            
      1450   302.27969      13.828755      0.0034851739   1              1            
      1500   262.57851      9.2567956      0.0034851739   1              1            
      1550   252.39492      1.2438631      0.0034851739   1              1            
      1600   247.18352      10.008173      0.0034851739   1              1            
      1650   290.30112     -2.1829055      0.0034851739   1              1            
      1700   272.78999     -57.305766      0.0034851739   1              1            
      1750   253.35258      24.729797      0.0034851739   1              1            
      1800   278.67832     -0.95017071     0.0034851739   1              1            
      1850   302.04743      16.002872      0.0034851739   1              1            
      1900   330.67188     -22.034206      0.0034851739   1              1            
      1950   342.64206      8.0075967      0.0034851739   1              1            
      2000   348.74388     -12.159899      0.0034851739   1              1            
      2050   300.48095      36.010534      0.0034851739   1              1            
      2100   275.017        8.7612294      0.0034851739   1              1            
      2150   303.92758      10.317032      0.0034851739   1              1            
      2200   308.89452      33.245012      0.0034851739   1              1            
      2250   265.74176      35.857111      0.0034851739   1              1            
      2300   273.40086      53.001626      0.0034851739   1              1            
      2350   287.74753     -0.14586562     0.0034851739   1              1            
      2400   278.7606      -8.20812        0.0034851739   1              1            
      2450   331.88979      39.02519       0.0034851739   1              1            
      2500   280.04041     -21.423589      0.0034851739   1              1            
      2550   388.81536     -12.350053      0.0034851739   1              1            
      2600   311.13468     -13.286785      0.0034851739   1              1            
      2650   325.07686      88.710881      0.0034851739   1              1            
      2700   319.08471      14.118288      0.0034851739   1              1            
      2750   261.72067      26.051439      0.0034851739   1              1            
      2800   281.03459     -21.201297      0.0034851739   1              1            
      2850   312.27342      4.3904047      0.0034851739   1              1            
      2900   274.81152     -12.739138      0.0034851739   1              1            
      2950   281.76873      11.199981      0.0034851739   1              1            
      3000   291.8377       48.595661      0.0034851739   1              1            
      3050   297.40212     -24.911752      0.0034851739   1              1            
      3100   341.48252      13.825136      0.0034851739   1              1            
      3150   347.5099      -10.452847      0.0034851739   1              1            
      3200   301.24901      26.553909      0.0034851739   1              1            
      3250   281.35392     -23.028031      0.0034851739   1              1            
      3300   279.82881     -53.225332      0.0034851739   1              1            
      3350   289.41016     -8.7866567      0.0034851739   1              1            
      3400   288.56923     -25.445059      0.0034851739   1              1            
      3450   259.59956      77.88466       0.0034851739   1              1            
      3500   295.99591      30.357393      0.0034851739   1              1            
      3550   302.1675      -5.103997       0.0034851739   1              1            
      3600   289.00244     -12.687621      0.0034851739   1              1            
      3650   333.89968     -33.124064      0.0034851739   1              1            
      3700   347.82328     -24.745583      0.0034851739   1              1            
      3750   354.51391      6.7131611      0.0034851739   1              1            
      3800   341.31124     -18.777474      0.0034851739   1              1            
      3850   320.48132      35.547595      0.0034851739   1              1            
      3900   326.8911      -49.153151      0.0034851739   1              1            
      3950   299.65543     -19.443322      0.0034851739   1              1            
      4000   308.97943      30.368402      0.0034851739   1              1            
      4050   251.46183     -17.518988      0.0034851739   1              1            
      4100   241.50223      22.103347      0.0034851739   1              1            
      4150   265.01178     -4.4952098      0.0034851739   1              1            
      4200   369.78569     -14.603579      0.0034851739   1              1            
      4250   348.20071     -33.060693      0.0034851739   1              1            
      4300   368.11836      11.897676      0.0034851739   1              1            
      4350   321.1145      -9.3124104      0.0034851739   1              1            
      4400   313.95395     -31.940883      0.0034851739   1              1            
      4450   280.50985      41.398853      0.0034851739   1              1            
      4500   289.36914     -2.3915112      0.0034851739   1              1            
      4550   318.52735     -5.0086703      0.0034851739   1              1            
      4600   308.68169     -13.642004      0.0034851739   1              1            
      4650   285.24153      35.314806      0.0034851739   1              1            
      4700   357.15021      8.8271927      0.0034851739   1              1            
      4750   359.11051     -59.672314      0.0034851739   1              1            
      4800   453.11584      0.54316266     0.0034851739   1              1            
      4850   392.52232      46.350736      0.0034851739   1              1            
      4900   310.42864      5.9002223      0.0034851739   1              1            
      4950   285.97355     -19.321724      0.0034851739   1              1            
      5000   309.41828      18.331381      0.0034851739   1              1            
      5050   324.96434     -27.143631      0.0034851739   1              1            
      5100   266.49422     -26.977074      0.0034851739   1              1            
      5150   295.35576     -14.271299      0.0034851739   1              1            
      5200   275.8961       14.057873      0.0034851739   1              1            
      5250   332.75955      26.04747       0.0034851739   1              1            
      5300   296.57102     -20.904181      0.0034851739   1              1            
      5350   264.68808      29.533914      0.0034851739   1              1            
      5400   293.373       -13.579532      0.0034851739   1              1            
      5450   290.55933      9.3458628      0.0034851739   1              1            
      5500   340.54834      8.8308229      0.0034851739   1              1            
      5550   336.08713     -6.9696582      0.0034851739   1              1            
      5600   331.77668     -7.9756709      0.0034851739   1              1            
      5650   307.8419      -10.263349      0.0034851739   1              1            
      5700   262.70119      78.855544      0.0034851739   1              1            
      5750   285.37985     -15.4042        0.0034851739   1              1            
      5800   267.44612     -30.053955      0.0034851739   1              1            
      5850   241.52125      3.2904907      0.0034851739   1              1            
      5900   265.13367      27.69901       0.0034851739   1              1            
      5950   277.95155      18.419031      0.0034851739   1              1            
      6000   309.62777     -20.054029      0.0034851739   1              1            
      6050   363.41588      16.435337      0.0034851739   1              1            
      6100   348.85793     -14.513241      0.0034851739   1              1            
      6150   323.73745      56.990265      0.0034851739   1              1            
      6200   338.66823     -19.93498       0.0034851739   1              1            
      6250   325.41329     -13.824943      0.0034851739   1              1            
      6300   279.82345     -9.0557197      0.0034851739   1              1            
      6350   285.90705      52.434161      0.0034851739   1              1            
      6400   260.34102     -15.766595      0.0034851739   1              1            
      6450   304.65686      7.5058044      0.0034851739   1              1            
      6500   265.02097      1.7203356      0.0034851739   1              1            
      6550   293.35057      1.8896974      0.0034851739   1              1            
      6600   284.06837     -9.3674953      0.0034851739   1              1            
      6650   307.29863     -2.3882614      0.0034851739   1              1            
      6700   336.20676      43.913926      0.0034851739   1              1            
      6750   291.53938     -16.749433      0.0034851739   1              1            
      6800   298.4418      -13.340335      0.0034851739   1              1            
      6850   264.13368     -11.219357      0.0034851739   1              1            
      6900   273.63109     -15.897238      0.0034851739   1              1            
      6950   282.64715      6.8275423      0.0034851739   1              1            
      7000   277.4091      -25.381099      0.0034851739   1              1            
      7050   278.07001      63.552969      0.0034851739   1              1            
      7100   293.33358      22.103462      0.0034851739   1              1            
      7150   308.36447     -27.212203      0.0034851739   1              1            
      7200   251.45077     -40.385347      0.0034851739   1              1            
      7250   317.57808      1.0302048      0.0034851739   1              1            
      7300   348.52627      48.392457      0.0034851739   1              1            
      7350   356.5821       27.933626      0.0034851739   1              1            
      7400   311.29835     -18.899768      0.0034851739   1              1            
      7450   274.24476     -19.41577       0.0034851739   1              1            
      7500   261.38075      1.2110527      0.0034851739   1              1            
      7550   299.78907     -17.64954       0.0034851739   1              1            
      7600   271.36191      25.99439       0.0034851739   1              1            
      7650   287.51241      1.532789       0.0034851739   1              1            
      7700   280.87778     -31.828432      0.0034851739   1              1            
      7750   312.22588      45.320976      0.0034851739   1              1            
      7800   312.73849      4.1022573      0.0034851739   1              1            
      7850   299.18742      50.272069      0.0034851739   1              1            
      7900   312.4916      -34.425195      0.0034851739   1              1            
      7950   284.5205       15.716375      0.0034851739   1              1            
      8000   248.39764     -7.1922339      0.0034851739   1              1            
      8050   242.65659     -32.701773      0.0034851739   1              1            
      8100   228.76112      54.351         0.0034851739   1              1            
      8150   308.67672     -15.835344      0.0034851739   1              1            
      8200   304.26746     -11.106867      0.0034851739   1              1            
      8250   338.67601      44.199636      0.0034851739   1              1            
      8300   308.59612     -9.6487546      0.0034851739   1              1            
      8350   287.08027      11.036122      0.0034851739   1              1            
      8400   319.79578     -78.918735      0.0034851739   1              1            
      8450   320.78978      57.275745      0.0034851739   1              1            
      8500   282.90803      33.716746      0.0034851739   1              1            
      8550   235.23686     -44.587941      0.0034851739   1              1            
      8600   265.62925      45.976855      0.0034851739   1              1            
      8650   260.35429     -9.3951434      0.0034851739   1              1            
      8700   236.16314      19.504695      0.0034851739   1              1            
      8750   291.51087     -13.996885      0.0034851739   1              1            
      8800   357.00246     -26.674845      0.0034851739   1              1            
      8850   327.72543      15.954838      0.0034851739   1              1            
      8900   321.17809     -14.794959      0.0034851739   1              1            
      8950   357.51102      39.861567      0.0034851739   1              1            
      9000   286.68385     -52.799636      0.0034851739   1              1            
      9050   283.96224      13.044025      0.0034851739   1              1            
      9100   304.04431      25.510777      0.0034851739   1              1            
      9150   261.33631     -18.611794      0.0034851739   1              1            
      9200   297.50501      25.733551      0.0034851739   1              1            
      9250   279.85018     -26.91045       0.0034851739   1              1            
      9300   336.07358      35.385228      0.0034851739   1              1            
      9350   326.27961     -36.941794      0.0034851739   1              1            
      9400   400.42857      7.5301492      0.0034851739   1              1            
      9450   296.80174      11.898673      0.0034851739   1              1            
      9500   275.98796      41.303486      0.0034851739   1              1            
      9550   278.56924      31.033397      0.0034851739   1              1            
      9600   260.24476     -11.416595      0.0034851739   1              1            
      9650   281.86065      12.60709       0.0034851739   1              1            
      9700   287.26789     -29.086626      0.0034851739   1              1            
      9750   290.82789      3.2830325      0.0034851739   1              1            
      9800   270.99421     -25.824595      0.0034851739   1              1            
      9850   385.1884       4.1048816      0.0034851739   1              1            
      9900   363.1711       18.815879      0.0034851739   1              1            
      9950   344.93572      17.375158      0.0034851739   1              1            
     10000   335.65852     -0.84087429     0.0034851739   1              1            
Loop time of 1.78856 on 4 procs for 10000 steps with 44 atoms

Performance: 483.070 ns/day, 0.050 hours/ns, 5591.087 timesteps/s, 246.008 katom-step/s
100.0% CPU use with 4 MPI tasks x no OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.0021174  | 0.066025   | 0.20024    |  31.5 |  3.69
Bond    | 0.0035593  | 0.2715     | 0.74757    |  58.6 | 15.18
Kspace  | 0.50386    | 1.0492     | 1.3455     |  33.6 | 58.66
Neigh   | 0.0079056  | 0.0079463  | 0.0079766  |   0.0 |  0.44
Comm    | 0.044284   | 0.08173    | 0.10388    |   8.1 |  4.57
Output  | 0.0021661  | 0.0024497  | 0.0031314  |   0.8 |  0.14
Modify  | 0.2648     | 0.29459    | 0.33479    |   5.5 | 16.47
Other   |            | 0.01514    |            |       |  0.85

Nlocal:             11 ave          41 max           0 min
Histogram: 3 0 0 0 0 0 0 0 0 1
Nghost:           27.5 ave          41 max           0 min
Histogram: 1 0 0 0 0 0 0 0 2 1
Neighs:         205.75 ave         820 max           0 min
Histogram: 3 0 0 0 0 0 0 0 0 1

Total # of neighbors = 823
Ave neighs/atom = 18.704545
Ave special neighs/atom = 9.9090909
Neighbor list builds = 225
Dangerous builds = 0

# write_restart restart_longrun
# write_data restart_longrun.data
Total wall time: 0:00:01
